From 479110ac45ce3833427e083dd62f96a0b41863d3 Mon Sep 17 00:00:00 2001
From: Marek Szuba <marek.szuba@ebi.ac.uk>
Date: Wed, 26 Sep 2018 12:54:06 +0100
Subject: [PATCH] Patched Compara and Variation test databases to schema
version 95
---
.../homo_sapiens/variation/meta.txt | 4 +-
.../homo_sapiens/variation/table.sql | 12 +++-
.../multi/compara/genome_db.txt | 72 +++++++++----------
.../t/test-genome-DBs/multi/compara/meta.txt | 6 +-
.../t/test-genome-DBs/multi/compara/table.sql | 15 ++--
.../mus_musculus/variation/meta.txt | 4 +-
.../mus_musculus/variation/table.sql | 12 +++-
7 files changed, 73 insertions(+), 52 deletions(-)
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
index 617810e94a..c00237682b 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
@@ -1,5 +1,5 @@
1 \N schema_type variation
-2 \N schema_version 94
+2 \N schema_version 95
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
@@ -32,3 +32,5 @@
32 \N patch patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
33 \N patch patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
34 \N patch patch_93_94_a.sql|schema version
+35 \N patch patch_94_95_a.sql|schema version
+36 \N patch patch_94_95_b.sql|create table to store allele synonyms
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
index f001fb43d3..c24098df16 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
@@ -20,6 +20,16 @@ CREATE TABLE `allele_code` (
UNIQUE KEY `allele_idx` (`allele`(1000))
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+CREATE TABLE `allele_synonym` (
+ `allele_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `variation_id` int(10) unsigned NOT NULL,
+ `hgvs_genomic` varchar(600) NOT NULL,
+ `name` varchar(255) NOT NULL,
+ PRIMARY KEY (`allele_synonym_id`),
+ UNIQUE KEY `variation_name_idx` (`variation_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
CREATE TABLE `associate_study` (
`study1_id` int(10) unsigned NOT NULL,
`study2_id` int(10) unsigned NOT NULL,
@@ -168,7 +178,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=35 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=37 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/multi/compara/genome_db.txt b/modules/t/test-genome-DBs/multi/compara/genome_db.txt
index 6f9da68b69..2026b3679f 100644
--- a/modules/t/test-genome-DBs/multi/compara/genome_db.txt
+++ b/modules/t/test-genome-DBs/multi/compara/genome_db.txt
@@ -1,11 +1,11 @@
-4 31033 takifugu_rubripes FUGU4 2007-11-Ensembl 0 1 \N \N \N \N 24 \N
-27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 1 \N \N \N \N 39 \N
-31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 1 \N \N \N \N 40 \N
+4 31033 takifugu_rubripes FUGU4 2007-11-Ensembl 0 0 \N \N \N \N 24 \N
+27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 0 \N \N \N \N 39 \N
+31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 0 \N \N \N \N 40 \N
33 9371 echinops_telfairi TENREC 2006-01-Ensembl 0 0 \N \N \N \N 40 \N
36 69293 gasterosteus_aculeatus BROADS1 2006-06-Ensembl 1 1 \N \N \N \N 40 \N
-37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 1 \N \N \N \N 41 \N
+37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 0 \N \N \N \N 41 \N
43 9258 ornithorhynchus_anatinus OANA5 2007-01-Ensembl 1 1 \N \N \N \N 42 \N
-46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 1 \N \N \N \N 44 \N
+46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 0 \N \N \N \N 44 \N
48 37347 tupaia_belangeri TREESHREW 2006-10-Ensembl 0 0 \N \N \N \N 43 \N
49 9365 erinaceus_europaeus HEDGEHOG 2006-10-Ensembl 0 0 \N \N \N \N 43 \N
55 42254 sorex_araneus COMMON_SHREW1 2007-04-Ensembl 0 0 \N \N \N \N 45 \N
@@ -14,7 +14,7 @@
61 9796 equus_caballus EquCab2 2007-09-Ensembl 1 1 \N \N \N \N 49 \N
65 99883 tetraodon_nigroviridis TETRAODON8 2007-11-Ensembl 1 1 \N \N \N \N 50 \N
67 9978 ochotona_princeps pika 2008-01-Ensembl 0 0 \N \N \N \N 50 \N
-69 10141 cavia_porcellus cavPor3 2008-03-Ensembl 0 1 \N \N \N \N 51 \N
+69 10141 cavia_porcellus cavPor3 2008-03-Ensembl 0 0 \N \N \N \N 51 \N
78 9358 choloepus_hoffmanni choHof1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
79 9813 procavia_capensis proCap1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
80 9739 tursiops_truncatus turTru1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
@@ -24,46 +24,46 @@
85 132908 pteropus_vampyrus pteVam1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
87 59729 taeniopygia_guttata taeGut3.2.4 2008-08-Ensembl 1 1 \N \N \N \N 53 \N
91 9315 macropus_eugenii Meug_1.0 2009-02-Ensembl 0 0 \N \N \N \N 55 \N
-98 9785 loxodonta_africana loxAfr3 2009-07-Ensembl 0 1 \N \N \N \N 57 \N
+98 9785 loxodonta_africana loxAfr3 2009-07-Ensembl 0 0 \N \N \N \N 57 \N
108 9986 oryctolagus_cuniculus OryCun2.0 2009-11-Ensembl 1 1 \N \N \N \N 60 \N
-109 9646 ailuropoda_melanoleuca ailMel1 2010-01-Ensembl 0 1 \N \N \N \N 60 \N
-111 28377 anolis_carolinensis AnoCar2.0 2010-09-Ensembl 1 1 \N \N \N \N 61 \N
+109 9646 ailuropoda_melanoleuca ailMel1 2010-01-Ensembl 0 0 \N \N \N \N 60 \N
+111 28377 anolis_carolinensis AnoCar2.0 2010-09-Ensembl 1 0 \N \N \N \N 61 \N
112 9103 meleagris_gallopavo UMD2 2010-09-Ensembl 1 1 \N \N \N \N 61 \N
-115 61853 nomascus_leucogenys Nleu1.0 2010-10-Ensembl 0 1 \N \N \N \N 62 \N
-116 8364 xenopus_tropicalis JGI_4.2 2010-09-Ensembl 0 1 \N \N \N \N 62 \N
-117 9483 callithrix_jacchus C_jacchus3.2.1 2010-02-Ensembl 1 1 \N \N \N \N 63 \N
-118 59463 myotis_lucifugus Myoluc2.0 2010-12-Ensembl 0 1 \N \N \N \N 63 \N
-120 7757 petromyzon_marinus Pmarinus_7.0 2011-02-Ensembl 0 1 \N \N \N \N 64 \N
-121 9305 sarcophilus_harrisii DEVIL7.0 2011-03-Ensembl 0 1 \N \N \N \N 64 \N
+115 61853 nomascus_leucogenys Nleu1.0 2010-10-Ensembl 0 0 \N \N \N \N 62 \N
+116 8364 xenopus_tropicalis JGI_4.2 2010-09-Ensembl 0 0 \N \N \N \N 62 \N
+117 9483 callithrix_jacchus C_jacchus3.2.1 2010-02-Ensembl 1 0 \N \N \N \N 63 \N
+118 59463 myotis_lucifugus Myoluc2.0 2010-12-Ensembl 0 0 \N \N \N \N 63 \N
+120 7757 petromyzon_marinus Pmarinus_7.0 2011-02-Ensembl 0 0 \N \N \N \N 64 \N
+121 9305 sarcophilus_harrisii DEVIL7.0 2011-03-Ensembl 0 0 \N \N \N \N 64 \N
122 9913 bos_taurus UMD3.1 2011-04-Ensembl 1 1 \N \N \N \N 64 \N
123 9595 gorilla_gorilla gorGor3.1 2009-08-Ensembl 1 0 \N \N \N \N 64 \N
-124 30611 otolemur_garnettii OtoGar3 2011-06-Ensembl 0 1 \N \N \N \N 65 \N
-125 9598 pan_troglodytes CHIMP2.1.4 2011-05-Ensembl 1 1 \N \N \N \N 65 \N
+124 30611 otolemur_garnettii OtoGar3 2011-06-Ensembl 0 0 \N \N \N \N 65 \N
+125 9598 pan_troglodytes CHIMP2.1.4 2011-05-Ensembl 1 0 \N \N \N \N 65 \N
126 8049 gadus_morhua gadMor1 2010-01-Ensembl 0 0 \N \N \N \N 65 \N
127 4932 saccharomyces_cerevisiae R64-1-1 2011-09-SGD 1 1 \N \N \N \N 65 \N
-128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 1 \N \N \N \N 66 \N
-129 7897 latimeria_chalumnae LatCha1 2011-09-Ensembl 0 1 \N \N \N \N 66 \N
-130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 1 \N \N \N \N 67 \N
-131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 1 \N \N \N \N 67 \N
-132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 1 \N \N \N \N 67 \N
-134 10090 mus_musculus GRCm38 2012-01-Ensembl 1 1 \N \N \N \N 68 \N
+128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 0 \N \N \N \N 66 \N
+129 7897 latimeria_chalumnae LatCha1 2011-09-Ensembl 0 0 \N \N \N \N 66 \N
+130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 0 \N \N \N \N 67 \N
+131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 0 \N \N \N \N 67 \N
+132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 0 \N \N \N \N 67 \N
+134 10090 mus_musculus GRCm38 2012-01-Ensembl 1 0 \N \N \N \N 68 \N
135 9615 canis_familiaris CanFam3.1 2011-11-Ensembl 1 1 \N \N \N \N 68 \N
-136 13735 pelodiscus_sinensis PelSin_1.0 2011-11-Ensembl 0 1 \N \N \N \N 68 \N
-137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 1 \N \N \N \N 69 \N
-138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 1 \N \N \N \N 69 \N
-139 9685 felis_catus Felis_catus_6.2 2011-12-Ensembl 1 1 \N \N \N \N 70 \N
-142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 1 \N \N \N \N 71 \N
+136 13735 pelodiscus_sinensis PelSin_1.0 2011-11-Ensembl 0 0 \N \N \N \N 68 \N
+137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 0 \N \N \N \N 69 \N
+138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 0 \N \N \N \N 69 \N
+139 9685 felis_catus Felis_catus_6.2 2011-12-Ensembl 1 0 \N \N \N \N 70 \N
+142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 0 \N \N \N \N 71 \N
143 6239 caenorhabditis_elegans WBcel235 2014-09-WormBase 1 1 \N \N \N \N 71 \N
-144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 1 \N \N \N \N 73 \N
-145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 1 \N \N \N \N 73 \N
-146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 1 \N \N \N \N 74 \N
+144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 0 \N \N \N \N 73 \N
+145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 0 \N \N \N \N 73 \N
+146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 0 \N \N \N \N 74 \N
147 9940 ovis_aries Oar_v3.1 2012-12-Ensembl 1 1 \N \N \N \N 74 \N
148 7918 lepisosteus_oculatus LepOcu1 2012-01-Ensembl 1 1 \N \N \N \N 74 \N
-149 9361 dasypus_novemcinctus Dasnov3.0 2013-06-Ensembl 0 1 \N \N \N \N 74 \N
-150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 1 \N \N \N \N 76 \N
-151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 1 \N \N \N \N 76 \N
-152 48698 poecilia_formosa PoeFor_5.1.2 2013-11-Ensembl 0 1 \N \N \N \N 76 \N
+149 9361 dasypus_novemcinctus Dasnov3.0 2013-06-Ensembl 0 0 \N \N \N \N 74 \N
+150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 0 \N \N \N \N 76 \N
+151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 0 \N \N \N \N 76 \N
+152 48698 poecilia_formosa PoeFor_5.1.2 2013-11-Ensembl 0 0 \N \N \N \N 76 \N
153 60711 chlorocebus_sabaeus ChlSab1.1 2014-03-Ensembl 1 1 \N \N \N \N 77 \N
-154 7955 danio_rerio GRCz10 2014-09-Ensembl 1 1 \N \N \N \N 80 \N
+154 7955 danio_rerio GRCz10 2014-09-Ensembl 1 0 \N \N \N \N 80 \N
155 10116 rattus_norvegicus Rnor_6.0 2014-09-Ensembl 1 1 \N \N \N \N 80 \N
156 7227 drosophila_melanogaster BDGP6 2014-05-FlyBase 1 1 \N \N \N \N 79 \N
diff --git a/modules/t/test-genome-DBs/multi/compara/meta.txt b/modules/t/test-genome-DBs/multi/compara/meta.txt
index 070a164b4e..6d5bed19ae 100644
--- a/modules/t/test-genome-DBs/multi/compara/meta.txt
+++ b/modules/t/test-genome-DBs/multi/compara/meta.txt
@@ -1,4 +1,4 @@
-53 \N schema_version 94
+57 \N schema_version 95
2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr
@@ -45,3 +45,7 @@
54 \N patch patch_93_94_a.sql|schema_version
55 \N patch patch_93_94_b.sql|homology_description_not_null
56 \N patch patch_93_94_c.sql|method_link_display_name
+58 \N patch patch_94_95_a.sql|schema_version
+59 \N patch patch_94_95_b.sql|remove_unused_indices
+60 \N patch patch_94_95_c.sql|genome_db_is_good_for_alignment
+61 \N patch patch_94_95_d.sql|node_type_within_species_speciation
diff --git a/modules/t/test-genome-DBs/multi/compara/table.sql b/modules/t/test-genome-DBs/multi/compara/table.sql
index 8b8d3b9a57..26bf1a0f65 100644
--- a/modules/t/test-genome-DBs/multi/compara/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/table.sql
@@ -40,9 +40,7 @@ CREATE TABLE `constrained_element` (
`score` double NOT NULL DEFAULT '0',
KEY `dnafrag_id` (`dnafrag_id`),
KEY `constrained_element_id_idx` (`constrained_element_id`),
- KEY `mlssid_idx` (`method_link_species_set_id`),
- KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`),
- KEY `mlssid_dfId_idx` (`method_link_species_set_id`,`dnafrag_id`)
+ KEY `mlssid_dfId_dfStart_dfEnd_idx` (`method_link_species_set_id`,`dnafrag_id`,`dnafrag_start`,`dnafrag_end`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `dnafrag` (
@@ -112,7 +110,6 @@ CREATE TABLE `family_member` (
`seq_member_id` int(10) unsigned NOT NULL,
`cigar_line` mediumtext,
PRIMARY KEY (`family_id`,`seq_member_id`),
- KEY `family_id` (`family_id`),
KEY `seq_member_id` (`seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -194,13 +191,12 @@ CREATE TABLE `gene_tree_node` (
PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`),
KEY `seq_member_id` (`seq_member_id`),
- KEY `root_id` (`root_id`),
KEY `root_id_left_index` (`root_id`,`left_index`)
) ENGINE=MyISAM AUTO_INCREMENT=100462681 DEFAULT CHARSET=latin1;
CREATE TABLE `gene_tree_node_attr` (
`node_id` int(10) unsigned NOT NULL,
- `node_type` enum('duplication','dubious','speciation','gene_split') DEFAULT NULL,
+ `node_type` enum('duplication','dubious','speciation','sub-speciation','gene_split') DEFAULT NULL,
`species_tree_node_id` int(10) unsigned DEFAULT NULL,
`bootstrap` tinyint(3) unsigned DEFAULT NULL,
`duplication_confidence_score` double(5,4) DEFAULT NULL,
@@ -277,7 +273,6 @@ CREATE TABLE `gene_tree_root_tag` (
`tag` varchar(255) DEFAULT NULL,
`value` mediumtext NOT NULL,
KEY `root_id_tag` (`root_id`,`tag`),
- KEY `root_id` (`root_id`),
KEY `tag` (`tag`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -288,7 +283,7 @@ CREATE TABLE `genome_db` (
`assembly` varchar(100) NOT NULL DEFAULT '',
`genebuild` varchar(100) NOT NULL DEFAULT '',
`has_karyotype` tinyint(1) NOT NULL DEFAULT '0',
- `is_high_coverage` tinyint(1) NOT NULL DEFAULT '0',
+ `is_good_for_alignment` tinyint(1) NOT NULL DEFAULT '0',
`genome_component` varchar(5) DEFAULT NULL,
`strain_name` varchar(40) DEFAULT NULL,
`display_name` varchar(255) DEFAULT NULL,
@@ -341,7 +336,6 @@ CREATE TABLE `genomic_align_tree` (
`distance_to_parent` double NOT NULL DEFAULT '1',
PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`),
- KEY `root_id` (`root_id`),
KEY `left_index` (`root_id`,`left_index`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
@@ -404,7 +398,6 @@ CREATE TABLE `homology_member` (
`perc_id` float unsigned DEFAULT '0',
`perc_pos` float unsigned DEFAULT '0',
PRIMARY KEY (`homology_id`,`gene_member_id`),
- KEY `homology_id` (`homology_id`),
KEY `gene_member_id` (`gene_member_id`),
KEY `seq_member_id` (`seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 MAX_ROWS=300000000;
@@ -436,7 +429,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=57 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=62 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
index ac149f5175..a405ae791a 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
@@ -1,5 +1,5 @@
1 \N schema_type variation
-2 \N schema_version 94
+2 \N schema_version 95
6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
@@ -59,3 +59,5 @@
65 \N patch patch_92_93_b.sql|Extend phenotype_ontology_accession mapped_by_attrib predefined set
66 \N patch patch_92_93_c.sql|Add new evidence attribs to the variation and variation_feature tables
67 \N patch patch_93_94_a.sql|schema version
+68 \N patch patch_94_95_a.sql|schema version
+69 \N patch patch_94_95_b.sql|create table to store allele synonyms
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
index 92c50d5dd0..aff0d32a92 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
@@ -20,6 +20,16 @@ CREATE TABLE `allele_code` (
UNIQUE KEY `allele_idx` (`allele`)
) ENGINE=MyISAM AUTO_INCREMENT=685956 DEFAULT CHARSET=latin1;
+CREATE TABLE `allele_synonym` (
+ `allele_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+ `variation_id` int(10) unsigned NOT NULL,
+ `hgvs_genomic` varchar(600) NOT NULL,
+ `name` varchar(255) NOT NULL,
+ PRIMARY KEY (`allele_synonym_id`),
+ UNIQUE KEY `variation_name_idx` (`variation_id`,`name`),
+ KEY `name_idx` (`name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
CREATE TABLE `associate_study` (
`study1_id` int(10) unsigned NOT NULL,
`study2_id` int(10) unsigned NOT NULL,
@@ -168,7 +178,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=68 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=70 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
--
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